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ENCSR904DTN: DNase-seq of mouse liver in constant darkness

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CREMA is a free online tool that recognizes most important transcription factors that change the chromatin state across different samples.

Results for Tbx4

Z-value: 0.31

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Transcription factors associated with Tbx4

Gene Symbol	Gene ID	Gene Info
Tbx4 Ensembl NCBI MGI UniProt	ENSMUSG00000000094.6	Tbx4

Correlations of motif activity and signal intensity at CREs associated with the motif's TFs:

This plot shows correlation between observed signal intensity of a CRE associated with the transcription factor across all samples and activity of the motif.

For each TF, only the top 5 correlated CREs are shown.

Gene	Promoter	Distance	Association probability	Pearson corr. coef.	P-value	Plot
Tbx4	chr11_85893909_85894085	2768	0.243929	-0.18	7.3e-01	Click!

Activity of the Tbx4 motif across conditions

Conditions sorted by the z-value of the Tbx4 motif activity

Move your cursor over a bar to see sample name and corresponding Z-value.

Top target CREs of the motif:

Cis Regulatory Element (CRE)	Target Score	Top associated gene	Gene Info	Distance of CRE to TSS	CRE/Gene association probability
chr16_46463130_46463327	0.55	Nectin3	nectin cell adhesion molecule 3	14718	0.27
chr3_31136392_31136619	0.22	Cldn11	claudin 11	13415	0.2
chr1_182500736_182501185	0.13	Gm37069	predicted gene, 37069	6804	0.14
chr19_30146095_30146265	0.11	Gldc	glycine decarboxylase	949	0.57
chr6_112873464_112873750	0.11	Srgap3	SLIT-ROBO Rho GTPase activating protein 3	44148	0.13
chr1_84059698_84059849	0.11	Pid1	phosphotyrosine interaction domain containing 1	6520	0.27
chr14_63265088_63265239	0.10	Gata4	GATA binding protein 4	5961	0.19
chr1_73909397_73909605	0.10	Tns1	tensin 1	18716	0.18
chr3_31136174_31136377	0.09	Cldn11	claudin 11	13645	0.2
chr11_53420114_53420567	0.09	Leap2	liver-expressed antimicrobial peptide 2	2830	0.12
chr9_108297063_108297481	0.09	Amt	aminomethyltransferase	350	0.72
chr11_20826808_20826959	0.09	Lgalsl	lectin, galactoside binding-like	3872	0.18
chr7_112498970_112499146	0.09	Parva	parvin, alpha	20643	0.2
chr2_128567912_128568063	0.09	Gm14006	predicted gene 14006	9753	0.13
chrX_143067335_143067542	0.09	Rtl9	retrotransposon Gag like 9	32156	0.2
chr11_86932862_86933027	0.08	Ypel2	yippee like 2	39080	0.14
chr4_97013861_97014018	0.08	Gm27521	predicted gene, 27521	96919	0.08
chr2_57332734_57332885	0.08	Gm13535	predicted gene 13535	57123	0.11
chr1_193271420_193271628	0.08	G0s2	G0/G1 switch gene 2	1693	0.19
chr4_132196053_132196243	0.07	Ythdf2	YTH N6-methyladenosine RNA binding protein 2	14661	0.08
chr15_75642798_75642949	0.07	2810039B14Rik	RIKEN cDNA 2810039B14 gene	389	0.75
chr13_34645504_34645908	0.07	Pxdc1	PX domain containing 1	2862	0.18
chr15_97161836_97161987	0.07	Gm32885	predicted gene, 32885	5311	0.27
chr15_10718434_10718784	0.07	4930556M19Rik	RIKEN cDNA 4930556M19 gene	758	0.66
chr3_31136684_31136995	0.07	Cldn11	claudin 11	13081	0.2
chr15_95872198_95872364	0.07	Gm25070	predicted gene, 25070	7536	0.19
chr11_22843395_22843546	0.07	Gm23772	predicted gene, 23772	3398	0.15
chr1_171454993_171455144	0.07	F11r	F11 receptor	7782	0.1
chr8_126727960_126728150	0.07	Gm45805	predicted gene 45805	30279	0.2
chr9_48675501_48675665	0.07	Nnmt	nicotinamide N-methyltransferase	70430	0.11
chr2_30386411_30386643	0.07	Miga2	mitoguardin 2	4583	0.1
chr2_30966491_30966663	0.07	Tor1a	torsin family 1, member A (torsin A)	1295	0.32
chr2_155390448_155390624	0.07	Ncoa6	nuclear receptor coactivator 6	6290	0.14
chr13_13753264_13753415	0.07	Lyst	lysosomal trafficking regulator	6603	0.21
chr4_15254591_15254742	0.07	Tmem64	transmembrane protein 64	11165	0.26
chr6_121859844_121860059	0.06	Mug1	murinoglobulin 1	18847	0.19
chr7_45488295_45488657	0.06	Dhdh	dihydrodiol dehydrogenase (dimeric)	329	0.63
chr9_77897902_77898083	0.06	Gm47824	predicted gene, 47824	3537	0.19
chr19_28928421_28928869	0.06	4430402I18Rik	RIKEN cDNA 4430402I18 gene	582	0.68
chr6_97294080_97294296	0.06	Frmd4b	FERM domain containing 4B	2927	0.28
chr7_27452561_27452934	0.06	Blvrb	biliverdin reductase B (flavin reductase (NADPH))	303	0.79
chr2_103454731_103454882	0.06	Elf5	E74-like factor 5	6068	0.19
chr1_58097131_58097333	0.06	Aox3	aldehyde oxidase 3	15898	0.18
chr14_21160817_21160968	0.06	Adk	adenosine kinase	84740	0.09
chr5_122494527_122494678	0.06	Gm43360	predicted gene 43360	306	0.77
chr1_93124444_93124635	0.06	Gm28086	predicted gene 28086	436	0.76
chr16_17892250_17892653	0.06	Dgcr2	DiGeorge syndrome critical region gene 2	758	0.3
chr8_122677096_122677352	0.06	Cbfa2t3	CBFA2/RUNX1 translocation partner 3	848	0.44
chr15_102181335_102181499	0.06	Csad	cysteine sulfinic acid decarboxylase	1556	0.24
chr13_60709526_60709699	0.06	Dapk1	death associated protein kinase 1	13199	0.17
chr14_73045910_73046229	0.06	Cysltr2	cysteinyl leukotriene receptor 2	3003	0.3
chr14_55468841_55469329	0.06	Dhrs4	dehydrogenase/reductase (SDR family) member 4	9673	0.1
chr1_130734318_130734676	0.06	AA986860	expressed sequence AA986860	2387	0.14
chr18_36726531_36726874	0.06	Cd14	CD14 antigen	36	0.94
chrX_60339140_60339308	0.06	Mir505	microRNA 505	55268	0.12
chr16_24460066_24460246	0.06	Lpp	LIM domain containing preferred translocation partner in lipoma	12065	0.21
chr11_75437280_75437567	0.06	Serpinf2	serine (or cysteine) peptidase inhibitor, clade F, member 2	1477	0.2
chr5_96455228_96455379	0.06	Gm33050	predicted gene, 33050	2440	0.34
chr16_16888784_16888935	0.06	Top3b	topoisomerase (DNA) III beta	1020	0.34
chr13_62927255_62927442	0.06	Gm48812	predicted gene, 48812	22094	0.13
chr4_144900352_144900520	0.06	Dhrs3	dehydrogenase/reductase (SDR family) member 3	7217	0.22
chr10_84424760_84424911	0.06	Nuak1	NUAK family, SNF1-like kinase, 1	15762	0.15
chr19_47580710_47580962	0.06	Slk	STE20-like kinase	817	0.55
chr18_84590910_84591391	0.06	Zfp407	zinc finger protein 407	1425	0.41
chr2_129101432_129101630	0.06	Polr1b	polymerase (RNA) I polypeptide B	504	0.68
chr11_102211338_102211489	0.06	Hdac5	histone deacetylase 5	7515	0.09
chr18_35849301_35849452	0.06	Cxxc5	CXXC finger 5	5311	0.11
chr16_10757949_10758100	0.06	Socs1	suppressor of cytokine signaling 1	27512	0.08
chr5_145861209_145861775	0.06	Cyp3a11	cytochrome P450, family 3, subfamily a, polypeptide 11	15199	0.15
chr9_71028459_71028669	0.06	Lipc	lipase, hepatic	76338	0.09
chr9_110703228_110703412	0.06	Ccdc12	coiled-coil domain containing 12	6574	0.12
chr11_120526901_120527125	0.06	Gm11789	predicted gene 11789	3541	0.08
chr11_106581287_106581448	0.06	Tex2	testis expressed gene 2	767	0.66
chr13_34646953_34647104	0.06	Pxdc1	PX domain containing 1	1540	0.29
chr11_107010555_107010708	0.05	Gm11708	predicted gene 11708	5891	0.14
chr6_30302088_30302239	0.05	Ube2h	ubiquitin-conjugating enzyme E2H	2359	0.22
chr3_83996881_83997402	0.05	Tmem131l	transmembrane 131 like	28913	0.2
chr1_75537481_75537658	0.05	Stk11ip	serine/threonine kinase 11 interacting protein	4531	0.1
chr15_75996647_75996807	0.05	Mapk15	mitogen-activated protein kinase 15	14	0.94
chr9_21730832_21730991	0.05	Ldlr	low density lipoprotein receptor	5196	0.13
chr10_21448325_21448476	0.05	Gm48386	predicted gene, 48386	2764	0.21
chr12_103956422_103956789	0.05	Serpina1e	serine (or cysteine) peptidase inhibitor, clade A, member 1E	293	0.83
chr2_158199719_158199870	0.05	1700060C20Rik	RIKEN cDNA 1700060C20 gene	7786	0.15
chr2_29437237_29437388	0.05	Gm24976	predicted gene, 24976	21882	0.15
chr17_66859168_66859319	0.05	Gm49940	predicted gene, 49940	2997	0.22
chr1_181005812_181005979	0.05	Ephx1	epoxide hydrolase 1, microsomal	9725	0.09
chr9_110582758_110582909	0.05	Setd2	SET domain containing 2	8949	0.13
chr6_5512042_5512193	0.05	Pdk4	pyruvate dehydrogenase kinase, isoenzyme 4	15808	0.27
chr11_109474178_109474329	0.05	Slc16a6	solute carrier family 16 (monocarboxylic acid transporters), member 6	655	0.45
chr12_17747270_17747517	0.05	Hpcal1	hippocalcin-like 1	19167	0.21
chr6_108837450_108837611	0.05	Edem1	ER degradation enhancer, mannosidase alpha-like 1	1120	0.56
chr4_107159322_107159488	0.05	Tceanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	18263	0.12
chr14_105253422_105253603	0.05	Gm22290	predicted gene, 22290	3502	0.18
chr4_106920101_106920437	0.05	Ssbp3	single-stranded DNA binding protein 3	2916	0.28
chr2_26553954_26554132	0.05	Gm13358	predicted gene 13358	4582	0.11
chr10_62980659_62980890	0.05	Rufy2	RUN and FYVE domain-containing 2	481	0.66
chr5_151232835_151233036	0.05	Stard13	StAR-related lipid transfer (START) domain containing 13	839	0.64
chr4_132489447_132489680	0.05	Gm12981	predicted gene 12981	20086	0.09
chr15_81360014_81360383	0.05	Slc25a17	solute carrier family 25 (mitochondrial carrier, peroxisomal membrane protein), member 17	529	0.71
chr17_29093649_29093812	0.05	Cdkn1a	cyclin-dependent kinase inhibitor 1A (P21)	39	0.91
chr18_6507791_6507957	0.05	Epc1	enhancer of polycomb homolog 1	8234	0.17
chr2_104123492_104123669	0.05	A930018P22Rik	RIKEN cDNA A930018P22 gene	811	0.53
chr13_113023428_113023726	0.05	Cdc20b	cell division cycle 20B	11534	0.08
chr3_116424764_116424926	0.05	Cdc14a	CDC14 cell division cycle 14A	813	0.56
chr2_92056065_92056235	0.05	2900072N19Rik	RIKEN cDNA 2900072N19 gene	3219	0.2
chr5_137986079_137986259	0.05	Azgp1	alpha-2-glycoprotein 1, zinc	4601	0.1
chr18_44633494_44633779	0.05	A930012L18Rik	RIKEN cDNA A930012L18 gene	28029	0.19
chr13_113602672_113602866	0.05	Snx18	sorting nexin 18	10872	0.17
chr2_126569048_126569199	0.05	Slc27a2	solute carrier family 27 (fatty acid transporter), member 2	4363	0.22
chr8_124589098_124589249	0.05	Capn9	calpain 9	13060	0.16
chr7_90141326_90141489	0.05	Gm45222	predicted gene 45222	4541	0.13
chr1_166410038_166410239	0.05	Pogk	pogo transposable element with KRAB domain	275	0.88
chr17_84990758_84990958	0.05	Ppm1b	protein phosphatase 1B, magnesium dependent, beta isoform	2815	0.25
chr6_58832026_58832202	0.05	Herc3	hect domain and RLD 3	253	0.93
chr19_42054767_42054919	0.05	4933411K16Rik	RIKEN cDNA 4933411K16 gene	2595	0.16
chr3_28025480_28025631	0.05	Pld1	phospholipase D1	5707	0.3
chr9_121906088_121906239	0.05	Ackr2	atypical chemokine receptor 2	1	0.95
chr7_141070384_141070555	0.05	B4galnt4	beta-1,4-N-acetyl-galactosaminyl transferase 4	133	0.9
chr19_55549970_55550134	0.05	Vti1a	vesicle transport through interaction with t-SNAREs 1A	169038	0.03
chr6_28736579_28736738	0.05	Snd1	staphylococcal nuclease and tudor domain containing 1	28032	0.19
chr2_31517780_31518546	0.04	Ass1	argininosuccinate synthetase 1	327	0.88
chr11_79230285_79230459	0.04	Wsb1	WD repeat and SOCS box-containing 1	12577	0.16
chr2_6074858_6075460	0.04	Upf2	UPF2 regulator of nonsense transcripts homolog (yeast)	24732	0.16
chr6_108102731_108102882	0.04	Sumf1	sulfatase modifying factor 1	24257	0.18
chr7_80111711_80111884	0.04	Gm45203	predicted gene 45203	837	0.46
chr11_100859548_100859739	0.04	Stat5a	signal transducer and activator of transcription 5A	13	0.97
chr12_99530270_99530421	0.04	Foxn3	forkhead box N3	33163	0.12
chr3_58685911_58686282	0.04	Siah2	siah E3 ubiquitin protein ligase 2	59	0.96
chr1_40790200_40790542	0.04	Mfsd9	major facilitator superfamily domain containing 9	286	0.89
chr4_144896227_144896412	0.04	Dhrs3	dehydrogenase/reductase (SDR family) member 3	3100	0.28
chr17_31383992_31384162	0.04	Pde9a	phosphodiesterase 9A	2133	0.25
chr11_50199089_50199272	0.04	Sqstm1	sequestosome 1	3774	0.13
chr9_66918909_66919116	0.04	Rab8b	RAB8B, member RAS oncogene family	675	0.66
chr13_46818454_46818623	0.04	Kif13a	kinesin family member 13A	9481	0.19
chr11_52364094_52364245	0.04	Vdac1	voltage-dependent anion channel 1	3034	0.23
chr14_73176868_73177019	0.04	Rcbtb2	regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 2	2492	0.24
chr2_168085703_168085998	0.04	Pard6b	par-6 family cell polarity regulator beta	4846	0.16
chr14_60784862_60785284	0.04	Mipep	mitochondrial intermediate peptidase	435	0.5
chr6_115464997_115465148	0.04	Gm44079	predicted gene, 44079	82	0.97
chr7_99176016_99176394	0.04	Dgat2	diacylglycerol O-acyltransferase 2	4088	0.15
chr10_128376319_128376655	0.04	Ankrd52	ankyrin repeat domain 52	628	0.38
chr6_70790677_70790915	0.04	Rpia	ribose 5-phosphate isomerase A	1207	0.42
chr1_134234537_134234704	0.04	Adora1	adenosine A1 receptor	42	0.97
chr9_115400503_115400904	0.04	Gm9487	predicted gene 9487	4446	0.15
chr6_149144748_149145030	0.04	Etfbkmt	electron transfer flavoprotein beta subunit lysine methyltransferase	3243	0.17
chr6_29516787_29517146	0.04	Kcp	kielin/chordin-like protein	9014	0.1
chr15_102442382_102442533	0.04	Amhr2	anti-Mullerian hormone type 2 receptor	2910	0.13
chr9_110390754_110390978	0.04	Ptpn23	protein tyrosine phosphatase, non-receptor type 23	391	0.77
chr17_27817988_27818406	0.04	Ilrun	inflammation and lipid regulator with UBA-like and NBR1-like domains	2255	0.2
chr14_47475021_47475196	0.04	Fbxo34	F-box protein 34	931	0.45
chr17_6828357_6828615	0.04	4933426B08Rik	RIKEN cDNA 4933426B08 gene	19977	0.14
chr8_124291752_124291934	0.04	Galnt2	polypeptide N-acetylgalactosaminyltransferase 2	3260	0.21
chr6_31400666_31400852	0.04	Mkln1	muskelin 1, intracellular mediator containing kelch motifs	1900	0.25
chr4_107159764_107160176	0.04	Tceanc2	transcription elongation factor A (SII) N-terminal and central domain containing 2	17698	0.12
chr12_76838153_76838373	0.04	Fntb	farnesyltransferase, CAAX box, beta	830	0.6
chr14_63143112_63143263	0.04	Ctsb	cathepsin B	7669	0.14
chr11_70741343_70741494	0.04	Gm12320	predicted gene 12320	13733	0.08
chr10_59884883_59885114	0.04	Dnajb12	DnaJ heat shock protein family (Hsp40) member B12	5372	0.16
chr1_88044569_88044899	0.04	AC087801.1	UDP glycosyltransferase 1 family (Ytg1) pseudogene	7134	0.08
chr3_143103418_143103577	0.04	Gm43614	predicted gene 43614	4451	0.28
chr7_144181012_144181177	0.04	Shank2	SH3 and multiple ankyrin repeat domains 2	5565	0.28
chr1_39545677_39545839	0.04	Snord89	small nucleolar RNA, C/D box 89	3096	0.14
chr16_41258426_41258587	0.04	Gm47276	predicted gene, 47276	40729	0.18
chr13_91748935_91749127	0.04	Gm27656	predicted gene, 27656	3075	0.19
chr13_51646798_51647087	0.04	Gm22806	predicted gene, 22806	1257	0.35
chr6_87846724_87847004	0.04	Cnbp	cellular nucleic acid binding protein	547	0.54
chr6_146473719_146473882	0.04	Gm15720	predicted gene 15720	10193	0.19
chr1_52816740_52816904	0.04	Inpp1	inositol polyphosphate-1-phosphatase	629	0.71
chr1_179587103_179587284	0.04	Cnst	consortin, connexin sorting protein	6197	0.2
chr12_17505824_17505980	0.04	Odc1	ornithine decarboxylase, structural 1	38892	0.11
chr9_69293134_69293313	0.04	Rora	RAR-related orphan receptor alpha	3541	0.3
chr7_13007324_13007475	0.04	Zbtb45	zinc finger and BTB domain containing 45	2401	0.12
chr18_39397194_39397356	0.04	Gm15337	predicted gene 15337	7850	0.22
chr2_30470118_30470322	0.04	Ier5l	immediate early response 5-like	3999	0.16
chr7_30947968_30948300	0.04	Hamp	hepcidin antimicrobial peptide	4102	0.08
chr9_44605679_44605889	0.04	Ddx6	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6	887	0.32
chr1_172082204_172082395	0.04	Copa	coatomer protein complex subunit alpha	230	0.7
chr1_159234206_159234548	0.04	Gm37115	predicted gene, 37115	1333	0.34
chr9_122355767_122356085	0.04	Abhd5	abhydrolase domain containing 5	4137	0.17
chr1_132349189_132349347	0.04	F730311O21Rik	RIKEN cDNA F730311O21 gene	7245	0.12
chr4_115088632_115088790	0.04	Pdzk1ip1	PDZK1 interacting protein 1	3	0.97
chr5_72652767_72652918	0.04	Nipal1	NIPA-like domain containing 1	5000	0.13
chr9_77749808_77749964	0.04	Gclc	glutamate-cysteine ligase, catalytic subunit	4649	0.16
chr2_18695636_18696007	0.04	Spag6	sperm associated antigen 6	1769	0.28
chr19_25402768_25403114	0.04	Kank1	KN motif and ankyrin repeat domains 1	3758	0.26
chr14_12103232_12103447	0.04	Ptprg	protein tyrosine phosphatase, receptor type, G	12179	0.23
chr3_98297519_98297734	0.04	Gm43189	predicted gene 43189	10638	0.14
chr17_34733622_34734232	0.04	C4b	complement component 4B (Chido blood group)	2172	0.12
chr4_137875186_137875337	0.04	Gm13012	predicted gene 13012	8151	0.2
chr7_100120840_100121149	0.04	Pold3	polymerase (DNA-directed), delta 3, accessory subunit	84	0.96
chr16_58514608_58514781	0.04	St3gal6	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	510	0.79
chr4_117330125_117330465	0.04	Rnf220	ring finger protein 220	30267	0.11
chr2_85071327_85071510	0.04	Tnks1bp1	tankyrase 1 binding protein 1	10454	0.12
chr15_59783186_59783337	0.04	Gm19510	predicted gene, 19510	11698	0.26
chr7_114089047_114089263	0.04	Gm45615	predicted gene 45615	2257	0.36
chr1_130761129_130761587	0.04	Gm28856	predicted gene 28856	5026	0.11
chr3_94581546_94582033	0.04	Snx27	sorting nexin family member 27	760	0.44
chr8_70719113_70719264	0.04	Gm3336	predicted gene 3336	645	0.45
chr9_72661312_72661471	0.04	Nedd4	neural precursor cell expressed, developmentally down-regulated 4	955	0.38
chr17_46484376_46484539	0.04	Ttbk1	tau tubulin kinase 1	162	0.91

Histogram of CRE-TSS distances for CREs targeted by :

Rank distribution of CRE target scores:

Distribution of target CREs across different genomic regions:

Network of associatons between targets according to the STRING database.

First level regulatory network of Tbx4

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

Total log-likelihood	Term	Description
0.1	GO:0019464	glycine catabolic process(GO:0006546) glycine decarboxylation via glycine cleavage system(GO:0019464)
0.1	GO:0071727	response to triacyl bacterial lipopeptide(GO:0071725) cellular response to triacyl bacterial lipopeptide(GO:0071727)
0.0	GO:0010046	response to mycotoxin(GO:0010046)
0.0	GO:0046544	development of secondary male sexual characteristics(GO:0046544)
0.0	GO:0046149	heme catabolic process(GO:0042167) pigment catabolic process(GO:0046149)
0.0	GO:0055118	negative regulation of cardiac muscle contraction(GO:0055118)
0.0	GO:0042732	D-xylose metabolic process(GO:0042732)
0.0	GO:1901078	negative regulation of relaxation of muscle(GO:1901078)

Gene overrepresentation in molecular function category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.0	0.0	GO:0005347	ATP transmembrane transporter activity(GO:0005347)